R-packages – /trunk/Matrix/src/lmer.h

Rev 1894 – More updates on lmer - still not quite correct

bates — Thu, 06 Oct 2005 03:07:23 +0000

bates – 6 file(s) modified
More updates on lmer - still not quite correct

~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Makefile
~ /trunk/Matrix/src/Syms.h

Rev 1876 – Modifications to mer2

bates — Mon, 03 Oct 2005 01:44:56 +0000

bates – 9 file(s) modified
Modifications to mer2

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/chm_common.c
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/Mutils.h

Rev 1851 – Temporary function mer2 to experiment with CHOLMOD-based mixed-effects

bates — Tue, 27 Sep 2005 00:50:35 +0000

bates – 8 file(s) modified
Temporary function mer2 to experiment with CHOLMOD-based mixed-effects

~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/lmer.R
x /trunk/Matrix/src/AMD/Source/Makefile.bak
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/SOURCES_C.mkf

Rev 1840 – Updated DEPS.mkf and some include files

bates — Mon, 19 Sep 2005 23:04:52 +0000

bates – 4 file(s) modified
Updated DEPS.mkf and some include files

~ /trunk/Matrix/src/dense.h
~ /trunk/Matrix/src/DEPS.mkf
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Makefile.win

Rev 1792 – Add "start" argument to lmer

bates — Tue, 06 Sep 2005 01:26:11 +0000

bates – 7 file(s) modified
Add "start" argument to lmer

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/man/lmer.Rd
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1779 – New simulate method for lmer objects

bates — Thu, 01 Sep 2005 13:46:21 +0000

bates – 7 file(s) modified
New simulate method for lmer objects

~ /trunk/Matrix/man/simulate.Rd
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1770 – Added simulate generic and method

bates — Tue, 30 Aug 2005 14:35:05 +0000

bates – 6 file(s) modified
Added simulate generic and method

+ /trunk/Matrix/man/simulate.Rd
~ /trunk/Matrix/R/AllGeneric.R
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1694 – Allow mcmcsamp on transformed parameters

bates — Sat, 06 Aug 2005 20:01:51 +0000

bates – 6 file(s) modified
Allow mcmcsamp on transformed parameters

~ /trunk/Matrix/data/sleepstudy.rda
~ /trunk/Matrix/man/mcmcsamp.Rd
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1672 – Added lmer_MCMCsamp to the C sources

bates — Sun, 24 Jul 2005 23:53:40 +0000

bates – 3 file(s) modified
Added lmer_MCMCsamp to the C sources

~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1668 – New sampling for glmerMCMC but intermediates are not appropriately PROTECTed

bates — Thu, 21 Jul 2005 16:41:42 +0000

bates – 4 file(s) modified
New sampling for glmerMCMC but intermediates are not appropriately PROTECTed

~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1667 – Added an rWishart function, which should later be moved to ...

bates — Thu, 21 Jul 2005 14:59:04 +0000

bates – 4 file(s) modified
Added an rWishart function, which should later be moved to the stats package

~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1642 – Preparing for glmmMCMC

bates — Thu, 07 Jul 2005 20:05:47 +0000

bates – 4 file(s) modified
Preparing for glmmMCMC

~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1610 – Adding MCMC capability (currently incomplete)

bates — Fri, 24 Jun 2005 23:06:33 +0000

bates – 5 file(s) modified
Adding MCMC capability (currently incomplete)

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1609 – Further development on AGQ and MCMC for glmm models

bates — Fri, 24 Jun 2005 15:38:43 +0000

bates – 5 file(s) modified
Further development on AGQ and MCMC for glmm models

~ /trunk/Matrix/INDEX
~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1593 – Setting up for AGQ

bates — Mon, 13 Jun 2005 19:45:04 +0000

bates – 4 file(s) modified
Setting up for AGQ

~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1592 – Factoring C code in preparation for AGQ

bates — Mon, 13 Jun 2005 01:22:28 +0000

bates – 5 file(s) modified
Factoring C code in preparation for AGQ

~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Syms.h

Rev 1591 – Moving devLaplace calculations to C code

bates — Fri, 10 Jun 2005 18:40:54 +0000

bates – 5 file(s) modified
Moving devLaplace calculations to C code

~ /trunk/Matrix/R/lmer.R
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/tests/lmer.R

Rev 1577 – Isolating and cleaning up the mer, lmer, and glmer functions

bates — Tue, 07 Jun 2005 23:03:34 +0000

bates – 5 file(s) modified
Isolating and cleaning up the mer, lmer, and glmer functions

~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/Mutils.h

Rev 1571 – Use mer objects; Replace REML slot by method slot

bates — Mon, 06 Jun 2005 15:51:24 +0000

bates – 4 file(s) modified
Use mer objects; Replace REML slot by method slot

~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Syms.h

Rev 1560 – Release 0.95-11

bates — Sun, 29 May 2005 02:15:35 +0000

bates – 3 file(s) modified
Release 0.95-11

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1540 – Fold bCrosstab.[ch] into lmer.[ch]

bates — Tue, 17 May 2005 17:45:24 +0000

bates – 4 file(s) modified
Fold bCrosstab.[ch] into lmer.[ch]

x /trunk/Matrix/src/bCrosstab.c
x /trunk/Matrix/src/bCrosstab.h
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1454 – changes related to Laplace approximation, including new function to compute ...

deepayan — Tue, 03 May 2005 16:08:26 +0000

deepayan – 4 file(s) modified
changes related to Laplace approximation, including new function to compute parts of the deviance in C code, which doesn't currently work

~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Syms.h

Rev 1448 – additions related to the Laplace approximation in glmm lmer models

deepayan — Fri, 29 Apr 2005 14:42:39 +0000

deepayan – 4 file(s) modified
additions related to the Laplace approximation in glmm lmer models

~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Syms.h

Rev 1217 – Added C function lmer_fitted

bates — Fri, 04 Mar 2005 03:49:53 +0000

bates – 3 file(s) modified
Added C function lmer_fitted

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 1054 – rearranging utility functions in the C code

bates — Thu, 10 Feb 2005 08:15:12 +0000

bates – 11 file(s) modified
rearranging utility functions in the C code

~ /trunk/Matrix/Done
~ /trunk/Matrix/R/dgBCMatrix.R
~ /trunk/Matrix/src/bCrosstab.c
~ /trunk/Matrix/src/dgBCMatrix.c
~ /trunk/Matrix/src/dgBCMatrix.h
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/Mutils.h
~ /trunk/Matrix/TODO

Rev 987 – renaming and rearranging classes

bates — Wed, 02 Feb 2005 19:11:51 +0000

bates – 28 file(s) modified
renaming and rearranging classes

~ /trunk/Matrix/src/bCrosstab.c
~ /trunk/Matrix/src/bCrosstab.h
+ /trunk/Matrix/src/dCholCMatrix.c (copied from /trunk/Matrix/src/sscChol.c@982)
+ /trunk/Matrix/src/dCholCMatrix.h (copied from /trunk/Matrix/src/sscChol.h@982)
~ /trunk/Matrix/src/DEPS.mkf
~ /trunk/Matrix/src/dgBCMatrix.c
~ /trunk/Matrix/src/dgBCMatrix.h
~ /trunk/Matrix/src/dgCMatrix.c
~ /trunk/Matrix/src/dgCMatrix.h
~ /trunk/Matrix/src/dgTMatrix.c
~ /trunk/Matrix/src/dgTMatrix.h
x /trunk/Matrix/src/dgTMatrix_to_dgCMatrix.c
x /trunk/Matrix/src/dgTMatrix_to_dgCMatrix.h
~ /trunk/Matrix/src/dpoMatrix.c
~ /trunk/Matrix/src/dpoMatrix.h
~ /trunk/Matrix/src/dsCMatrix.c
~ /trunk/Matrix/src/dsCMatrix.h
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/SOURCES_C.mkf
x /trunk/Matrix/src/sscChol.c
x /trunk/Matrix/src/sscChol.h
~ /trunk/Matrix/src/sscCrosstab.c
~ /trunk/Matrix/src/sscCrosstab.h
+ /trunk/Matrix/src/triplet_to_col.c (copied from /trunk/Matrix/src/dgTMatrix_to_dgCMatrix.c@982)
+ /trunk/Matrix/src/triplet_to_col.h (copied from /trunk/Matrix/src/dgTMatrix_to_dgCMatrix.h@982)

Rev 984 – renaming and rearranging classes

bates — Wed, 02 Feb 2005 17:20:55 +0000

bates – 8 file(s) modified
renaming and rearranging classes

~ /trunk/Matrix/src/bCrosstab.c
x /trunk/Matrix/src/cscBlocked.c
x /trunk/Matrix/src/cscBlocked.h
+ /trunk/Matrix/src/dgBCMatrix.c (copied from /trunk/Matrix/src/cscBlocked.c@982)
+ /trunk/Matrix/src/dgBCMatrix.h (copied from /trunk/Matrix/src/cscBlocked.h@982)
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h

Rev 977 – Renaming and reorganizing classes

bates — Wed, 02 Feb 2005 14:33:51 +0000

bates – 32 file(s) modified
Renaming and reorganizing classes

~ /trunk/Matrix/src/bCrosstab.c
~ /trunk/Matrix/src/bCrosstab.h
~ /trunk/Matrix/src/cscBlocked.c
~ /trunk/Matrix/src/cscBlocked.h
~ /trunk/Matrix/src/cscMatrix.c
~ /trunk/Matrix/src/cscMatrix.h
~ /trunk/Matrix/src/geMatrix.c
~ /trunk/Matrix/src/geMatrix.h
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/LU.c
~ /trunk/Matrix/src/LU.h
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/Mutils.h
~ /trunk/Matrix/src/poMatrix.c
~ /trunk/Matrix/src/poMatrix.h
~ /trunk/Matrix/src/sscChol.h
~ /trunk/Matrix/src/sscCrosstab.c
~ /trunk/Matrix/src/sscCrosstab.h
~ /trunk/Matrix/src/sscMatrix.c
~ /trunk/Matrix/src/sscMatrix.h
~ /trunk/Matrix/src/syMatrix.c
~ /trunk/Matrix/src/syMatrix.h
~ /trunk/Matrix/src/triplet.c
~ /trunk/Matrix/src/triplet.h
~ /trunk/Matrix/src/triplet_to_col.c
~ /trunk/Matrix/src/triplet_to_col.h
~ /trunk/Matrix/src/trMatrix.c
~ /trunk/Matrix/src/trMatrix.h
~ /trunk/Matrix/src/tscMatrix.c
~ /trunk/Matrix/src/tscMatrix.h

Rev 952 – Add an externally accessible entry point to lmer_Crosstab

bates — Sat, 29 Jan 2005 14:14:01 +0000

bates – 1 file(s) modified
Add an externally accessible entry point to lmer_Crosstab

~ /trunk/Matrix/src/lmer.h

Rev 934 – Change char flags to cblas enum types

bates — Fri, 21 Jan 2005 12:17:56 +0000

bates – 6 file(s) modified
Change char flags to cblas enum types

~ /trunk/Matrix/src/bCrosstab.c
~ /trunk/Matrix/src/cscBlocked.c
~ /trunk/Matrix/src/cscBlocked.h
~ /trunk/Matrix/src/lmer.c
~ /trunk/Matrix/src/lmer.h
~ /trunk/Matrix/src/Mutils.h

Rev 883 – Change to the lmer representation

bates — Mon, 03 Jan 2005 19:05:11 +0000

bates – 13 file(s) modified
Change to the lmer representation

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/src/bCrosstab.c
~ /trunk/Matrix/src/cscBlocked.c
~ /trunk/Matrix/src/cscBlocked.h
~ /trunk/Matrix/src/cscMatrix.h
~ /trunk/Matrix/src/init.c
+ /trunk/Matrix/src/lmer.c (copied from /trunk/Matrix/src/lmeRep.c@875)
+ /trunk/Matrix/src/lmer.h (copied from /trunk/Matrix/src/lmeRep.h@873)
x /trunk/Matrix/src/lmeRep.c
x /trunk/Matrix/src/lmeRep.h
~ /trunk/Matrix/src/sscCrosstab.h
~ /trunk/Matrix/src/triplet_to_col.c

Rev 873 – Working on the lmer classes

bates — Tue, 28 Dec 2004 14:51:42 +0000

bates – 12 file(s) modified
Working on the lmer classes

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/src/bCrosstab.c
~ /trunk/Matrix/src/bCrosstab.h
~ /trunk/Matrix/src/init.c
~ /trunk/Matrix/src/lmeRep.c
~ /trunk/Matrix/src/lmeRep.h
~ /trunk/Matrix/src/ssclme.c
~ /trunk/Matrix/src/ssclme.h
~ /trunk/Matrix/src/Syms.h

Rev 572 – Adding lmeRep_L_sm and support routines

bates — Tue, 12 Oct 2004 15:44:15 +0000

bates – 4 file(s) modified
Adding lmeRep_L_sm and support routines

~ /trunk/Matrix/src/cscBlocked.c
~ /trunk/Matrix/src/cscBlocked.h
~ /trunk/Matrix/src/lmeRep.c
~ /trunk/Matrix/src/lmeRep.h

Rev 561 – Add registration of .Call functions

bates — Mon, 04 Oct 2004 17:13:29 +0000

bates – 15 file(s) modified
Add registration of .Call functions

~ /trunk/Matrix/ChangeLog
~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/R/sscMatrix.R
~ /trunk/Matrix/src/cscMatrix.h
~ /trunk/Matrix/src/lmeRep.c
~ /trunk/Matrix/src/lmeRep.h
~ /trunk/Matrix/src/Makefile
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/Mutils.h
~ /trunk/Matrix/src/ssclme.h
~ /trunk/Matrix/src/sscMatrix.c
~ /trunk/Matrix/src/syMatrix.c
~ /trunk/Matrix/src/syMatrix.h
~ /trunk/Matrix/src/trMatrix.c

Rev 488 – New version

bates — Tue, 31 Aug 2004 19:13:33 +0000

bates – 5 file(s) modified
New version

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/src/lmeRep.c
~ /trunk/Matrix/src/lmeRep.h
~ /trunk/Matrix/src/Mutils.h

Rev 466 – Remove taucs, add lmeRep, new release

bates — Tue, 24 Aug 2004 02:08:08 +0000

bates – 16 file(s) modified
Remove taucs, add lmeRep, new release

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/INDEX
+ /trunk/Matrix/man/lmeRep-class.Rd
~ /trunk/Matrix/man/sscChol-class.Rd
~ /trunk/Matrix/R/AllClass.R
~ /trunk/Matrix/src/cscMatrix.h
~ /trunk/Matrix/src/lmeRep.c
~ /trunk/Matrix/src/lmeRep.h
~ /trunk/Matrix/src/Makefile
~ /trunk/Matrix/src/Makefile.win
~ /trunk/Matrix/src/sscMatrix.c
~ /trunk/Matrix/src/sscMatrix.h
x /trunk/Matrix/src/taucs
x /trunk/Matrix/src/taucs_utils.c
x /trunk/Matrix/src/taucs_utils.h
x /trunk/Matrix/src/utils.c

Rev 464 – Add the lmeRep class

bates — Fri, 20 Aug 2004 16:27:15 +0000

bates – 9 file(s) modified
Add the lmeRep class

~ /trunk/Matrix/DESCRIPTION
~ /trunk/Matrix/NAMESPACE
~ /trunk/Matrix/R/AllClass.R
+ /trunk/Matrix/R/lmeRep.R
+ /trunk/Matrix/src/lmeRep.c
+ /trunk/Matrix/src/lmeRep.h
~ /trunk/Matrix/src/Makefile
~ /trunk/Matrix/src/Mutils.c
~ /trunk/Matrix/src/Mutils.h